DR.

FREDERICK: CELL AND MOLECULAR BIOLOGY

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CHAPTER 2: Chemical Context of Life
Structure = function
Body works through chemical reactions

Chemical reactions - molecules making and breaking bonds

structure of molecule directly relates to its interactions and functions

elements are made up of atoms - # of protons define an element (OXYGEN IS OXYGEN BC 8 PROTONS)

change in number of protons = change in element

each element consists of a certain kind of atom that is different from the atoms of other elements
92 elements (25 essential, cannot live without)

trace elements - required in minute quantities

o iron, iodide

biology --> balance

compound - substance consisting of 2 or more different elements combined in a fixed ratio

matter --> elements --> atoms --> neutrons, protons, electrons

Elements' properties depend on the structure of the atoms

structure of the atom depends on subatomic particles

atomic mass = weight neutrons + weight protons (electrons minimal mass, not counted)

Dalton (atomic mass unit, amu) (UNIT OF MASS) 1.7x10-24 g

o 1 proton or neutron = 1 dalton

atomic number = # of protons

all atoms of a particular element have the same number of protons in their nuclei
change the number of electrons or neutrons - remains same element

Atoms - neutral electrical charge, unless otherwise indicated

number of protons = number of electrons

IONS WILL HAVE DIFFERENT NUMBER OF PROTONS VS ELECTRONS - CHANGED ELECTRON

NUMBER
mass number = number of neutrons + number of protons

Isotopes

same element - different number of neutrons

o atomic number stays same
o atomic mass will differ

radioactive isotopes
stable isotopes do not lose particles
radioactive isotope - unstable

nucleus spontaneously decays

o gives off particles and energy
o gives off proton - change element
radioactive carbon --> boron

Radioactive tracers

used to follow metabolic rxns

kidney disorders - inject small dose into blood, measure amount in urine
detect cancerous tissue - PET scanner

Section 3: chemical rxns and energy

atom's ability to interact with other molecules - chemical rxn

atoms collide - only electrons interact

takes energy to interact

energy -capacity to cause change (do work)

kinetic energy - energy of movement

potential energy - energy matter possesses due to stationary state
greatest potential energy -- unstable
lowest potential energy -- stable

electrons have potential energy

amount of energy varies

o depends on how electrons are arranged in relation to the nucleus

negative electrons attracted to positive protons

location of electron -- further from nucleus = greater potential energy closer = least potential energy

takes work to move an electron farther away from the nucleus

matter moves to the lowest possible state of potential energy

(HIGH CONCENTRATION TO LOW CONCENTRATION)

LOW POTENTIAL ENERGY = STABLE

HIGH POTENTIAL ENERGY = UNSTABLE

Energy levels - electrons

Electrons can have changes in potential energy - occurs in fixed "steps"
electron shells
electron level - how much potential energy electron possesses
increase energy - move further from nucleus
electrons can move from one shell to another
absorbs energy - moves further way from nucleus
lose energy - move closer to nucleus

chemical properties -reactivity

chemical behavior determined by electron configuration
distribution of electrons in atom's electron shells
chemical behavior depends on number of electrons in the outermost shell (valence shell)
valence electrons - electrons in the outermost shell
electron shells
shell 1-2 electrons
shell 2-8 electrons
shell 3-8 electrons
atoms that have same number of valence electrons exhibit similar chemical behavior
full valence shell - stable, unreactive, inert
incomplete valence shell - reactive
no real defined space (shells not physical thing)
orbitals - pathways
each orbital can hold 2 electrons

section 4:chemical bonds

unpaired electrons - reactive
combine other atoms to fill valence shells

covalent - strongest
ionic
hydrogen - weakest

covalent bonds
pair of valence electrons is shared
orbitals overlap
molecule - 2 or more atoms held together by a covalent bond
compound - consists of 2 or more atoms
water molecule (compound)
bonding capacity - number of covalent bonds the atom can form
bonding capacity = valence
valence - number of electrons it takes to fill the valence shell
(EXAMPLE: OXYGEN'S VALENCE = 2)
nonpolar covalent bond - electrons are shared equally (no charge)
polar covalent bond - electros are not shared equally (charge)
electronegativity - attraction of an atom for the electrons in a covalent bond
more electronegative an atom, more strongly it pulls shared electrons to itself
oxygen and nitrogen very electronegative

high electronegativity - oxygen, nitrogen

low electronegativity - carbon, hydrogen
non-polar bonds - O-O, N-N, C-C, H-H, C-H
polar bonds - O-C, O-H, N-C, N-H

polar molecule - molecule with polar covalent bonds

nonpolar molecule - molecule with nonpolar covalent bonds

ionic bonds

attraction between oppositely charged molecules or atoms

ion-charged atom or molecule -> lose/gain electron
positive charge - cation
negative charge - anion
transferring of electron is NOT the bond
DNA hydrogen bonds galore
Shape is important bc determines how molecules recognize and interact with specificity
END CHAPTER 2

Chapter 3: Properties of Water

Hydrogen bonding responsible for water properties
Water is necessary in chemical reactions critical to sustain life
Water is unique only substance exists in natural environment in all 3 physical states of matter
Structure of water responsible for its unique properties
Polar molecule opposite ends of the molecule have opposite charges
Unique properties arise from attractions between polar molecules

hydrogen bonding

Water Properties
4 properties

cohesion
o binds a substance together
o Water molecules attracted to each other through hydrogen bonds
Liquid: Hydrogen bonds constantly breaking and re-forming
At any instance, a substantial percentage of all water molecules are bonded together
Makes water more structured than other liquids
o Contributes to transport of water and dissolved nutrients against gravity in plants
o Adhesion
Clinging of one substance to another
- water adheres to walls of cells, counters downward pull of gravity
o surface tension
measure of how difficult it is to stretch or break the surface of a liquid
- water has greater surface tension than most liquids
interface between water and air ordered arrangement of water molecules
- hydrogen bonded to one another and water below
- behaves like an invisible film
Essential for transfer of energy from wind to water to create waves
Waves necessary for rapid oxygen diffusion in lakes and oceans
moderation of temperature
o moderates air temperature by absorbing heat from air that is warmer and releasing stored heat to
air that is cooler

o
o
o
o
o
o
o
o
o

o
o
o
o
o

o
o
o

hot to cold; high concentration of thermal energy to low concentration

heat bank
stores heat
can absorb or release a large amount of heat with only a slight change in its own
temperature
Kinetic energy energy of motion
Atoms and molecules have kinetic energy always in motion
Faster a molecule moves, more kinetic energy required
Heat total amount of kinetic energy due to molecule motion in a body of matter
Temperature measures the intensity of heat due to the average kinetic energy of molecules
HEAT IS A FORM OF ENERGY DEPENDS ON VOLUME OF THE MATTER
TEMPERATURE IS A MEASURE OF ENERGY REGARDLESS OF VOLUME
As average speed of molecules increase, temperature increases
Heat and temperature related
Heat total amount of kinetic energy
Temperature measure of the average kinetic energy (how fast molecules are moving
- Human body has higher temperature than ocean, but ocean contains far more
heat
Energy flows from high to low concentration
**********ENERGY, HEAT, MOLECULES, ETC. ALL FLOW FROM HIGH TO LOW
CONCENTRATIONS***********
Calorie (cal) amount of heat it takes to raise the temperature of 1 gram of water by 1 degree
Celsius
Kilocalorie (kcal) 1,000 calories, quantity of heat required to raise the temperature of 1 kilogram
of water by 1 degree Celsius
Joule
1 J = 0.239 cal
1 cal 4.184 J
Specific heat
Amount of heat that must be absorbed or lost for 1 g of that substance to change its
temperature by 1 degree Celsius
Water specific heat 1 cal/g/degree Celsius
- Unusually high specific heat
- Takes a lot of heat to raise temp
- Water can absorb a lot of heat and release a lot of heat without changing its
temperature much
Specific heat of water so high because of hydrogen bonding
- Heat absorbed break H-bonds
- Heat released form H-bonds
Large bodies of water absorb and store huge amounts of heat from the sun; warming up
water
Night/winter water releases heat, warming air
Stabilizes ocean temperature, directly affects air; keeps earths temperature within limits
to permit life
Water regulates body temperature
Evaporation liquid to gas
Liquid molecules all attracted to each other, molecules start moving fast enough, break all bonds,
depart the liquid into the air has a gas
Temperature AVERAGE kinetic energy of molecules
Have some molecule smoving fast even at low temperature
Glass of water is evaporating at room temperature
Heat liquid (providing energy) average kinetic energy increasing quicker

***SOLIDS HAVE LEAST AMOUNT OF ENERGY, GASES HAVE THE MOST,

LIQUIDS ARE IN THE MIDDLE***
o Heat of vaporization
Moderate earths climate
- Tropical seas absorb a large amount fo solar heat
- Water evaporates moist, warm tropical air
Warm air circulates poleward releasing heat
- Lose heat, forming more H-bonds
- Gas- liquid rain
Surface water that is evaporating highest kinetic energy (hottest)
- Evaporative cooling average temperature drops
o Contributes to stability of temperature in lakes and ponds
o Prevents terrestrials from overheating
Water evaporates from plant leaves, prevents tissue from
becoming too warm in sun
Sweat cools ppl off; evaporating off skin, dissipating body
heat
o High humidity is hotter
High concentration of water vapor in air, inhibits evaporation
of sweat from the body
high to low (air dry = low water vapor = sweat
vaporizes easily
Air is moist = high water vapor = sweat will not
evaporate
expansion upon freezing
o water is less dense as a solid than a liquid
solids have more molecules packed tightly together
more mass heavy
- WATER IS OPPOSITE
o Water is lighter as a solid
Water expands instead of contracting below 4 degree Celsius
HYDROGEN BONDING
o Behaves like other liquids when at 4 degrees Celsius or above
Expands as it warms, contracts as it cools
o BELOW 4 degrees Celsius behaves uniquely
Starts expanding
- Water is densest at 4 degrees Celsius
o Freezing molecules are no longer moving vigorously enough to break Hydrogen bonds
o 0 degrees Celsius water locks into crystal lattice
Each molecule bonds to 4 partners
- Hydrogen bond are a set distance apart
- Ice is 10% less dense than liquid water at 4 degrees Celsius
o 10% fewer molecules for same volume
o IF ICE SANK, LIFE AS WE KNOW IT WOULD CEASE TO EXIST
o Ice floats, water below is warming, insulated
Prevents freezing, creatures can live underneath
versatility as a solvent
o transport substance throughout earth and body
o solution
liquid that is completely homogenous mixture of 2 or more substances
- salt water, salt dissolves and the concentration is then uniform throughout the
water

solvent dissolving agent (water)

solute substance that is dissolved (salt)
aqueous solution water is solvent
NaCl- ionic compound (Na+ cation, Cl- anion)
Surface of salt crystal charges
o Attracted to water- charge
Oxygen (-) attracted to Na+
Hydrogen (+) attracted to Clo Water molecule surrounds individual Na+ or Cl- ions
Sphere of water molecules (Hydration Shell)
Separates them, shields them from one another
o Compound does not need to be ionic to be dissolved
o Nonionic polar molecules sugar molecules
Ionic compound each individual atom has a charge
Nonionic compound atoms have no charge
Polar molecule charge difference throughout the molecule
Hydrophilic and hydrophobic substances
o Hydrophilic water loving
Any substance with attraction to water (charges)
- Ionic or polar substances
- Dissolve in water
Some large molecules inside of cells do not dissolve
- Remain suspended in liquid portion of cell
Colloid stable suspension of fine particles in a liquid
EXAMPLE: COTTON
- Cellulose very large molecules with regions of partial positive/negative
charges
- Water will adhere to cellulose
o Hydrophobic water fearing
Nonionic and nonpolar substances repel water
olive oil, cell membranes, lipids, etc
o ********LIKE DISSOLVES LIKE**********
Charged molecules attracted to charged molecules
- Hydrophilic molecules
- Ionic substances
- Polar molecules polar covalent bond
Uncharged molecules attracted to uncharged molecules
- Hydrophobic molecules
- Nonpolar molecules nonpolar bonds
- NO CHARGE
MOLECULAR MASS:
o Biochemistry
Almost every chemical rxn in body occurs in water
To understand rxn
- Must know how many atoms and molecules are involved
- USE MASS TO DETERMINE NUMBER OF MOLECULES
o Mass of atom = # of protons + # of neutrons (atomic mass)
o Molecular mass sum of the masses of all the atoms in a molecule
Water: 2 hydrogen atoms and 1 oxygen
H2O molecular formula
o Avogadros number
6.02x1023
o Mole = quantity
o
o
o
o

1 mol of any substance = molecular mass (g)

Molarity
Number of moles of solute per liter (L) of solution (concentration)
o Molecular formula atoms which make 1 molecule
o Atomic mass mass of 1 atom
o Molecular mass mass of 1 molecule (daltons)
o Molar mass mass of 1 mol of a substance (grams)
o Molarity number of solutes (moles) in 1 liter of solution
o Molar mass = g/mol
o Molarity (M) = moles/L
DISSOCIATION OF WATER MOLECULES:
o hydrogen can give up an electron and leave the water molecule - H+ (proton)
hydrogen ion
o leaves behind OH hydroxide ion
o Reversible rxn
state of equilibrium
- water dissociates at the same rate it is re-formed
- at the equilibrium point [H2O] greatly exceeds the [H+] and [OH-]
ion concentration in pure water
- 10-7 M (1 L of H2O 1 ten-millionth of a mole) - for both
- very reactive ions
- unbalanced by acids and bases
- 0.0000001mol / 1 L
o Acid
solute that donates H+
- increases H+ concentration of a solution
- HCl --> H+ + Clo Base
solute that reduces the [H+]
- use up H+
- Donate OH- Basic solution --> solution OH-> H+
o Neutral solution
[H+] = [OH-]
pH Scale
o measures concentration of HYDROGEN ions
o in any aqueous solution @ 25 degrees C, the product of [H+] and [OH-] is constant at 10-14 M
o Balance: [H+] = 10-5 M [OH-] = 10-9 M
o [H+] and [OH-] can vary up to a factor of 100 trillion +
use logarithms for pH scale (log scale)
scale of measurement uses the logarithm of physical quantity instead of the quantity itself
o pH = negative logarithm (base 10) of the hydrogen ion concentration
pH = -log [H+]
[H+] = 10-7
pH = -log 10-7 = -(-7) = 7
o Low pH = higher [H+]
Low pH = acidic solution
High pH = basic solution
Log scale - 10 times difference from one pH value to the next
o pH of 3 is 1000x more acidic than pH 6
Buffers
o internal pH around 7
o
o

most biological fluids pH 6-8

- stomach acid pH = 2
slight change in pH harmful b/c chemical processes of the cell very sensitive to concentrations of
H+ and OHbuffers keep pH relatively constant
minimize the change in [H+] and [OH-]
Blood pH 7.4
drops to 7 or rises to 7.8 you will only last a few minutes
blood has buffering capacity
buffer either accepts H+ when they are in excess or donates H+ when they are depleted
H2CO3 carbonic acid - blood buffer

o
o
o

o
o

END CHAPTER 3

Chapter 4: Carbon and the Molecular Diversity of Life

Carbon - backbone of biological molecules

o all living organisms are composed of carbon-based molecules
cells 70-95% water
5-30% carbon-based compounds
proteins, DNA, carbohydrates, lipids
o Carbon interacts with other atoms diversely
Form large, complex, different molecules
Carbon is source of life
o carbon cycle
plants use CO2 + sunlight = starches/sugars (GLUCOSE)
Energy + O2
Eating plant releases energy, metabolic processes
Complete cycle - breathe out CO2
Organic chemistry
o study of carbon compounds
o any compound containing carbon -- organic
simplex or complex
Contain H atoms
o % of major elements (C, H, O, N, S, P) found in similar proportions between organisms
Carbon diversity
o Bonds to 4 other atoms
o Electron configuration determines the kinds and number of bonds an atom will form with other
atoms
Carbon bonds
o 4 valence electrons

forms 4 covalent bonds - tetravalence

large, complex molecules possible
o single covalent bond - one electron shared
o molecules with multiple carbons - each C bonds to 4 other atoms
tetrahedral shape - angles 109.5 degrees
single covalent bonds
**** NONPOLAR BONDS BETWEEN C-H (NO CHARGE)****
o 2 carbon atoms joined by a double bond - molecule has a flat shape
o share 2 electrons - same plane
Hydrocarbon chains - bonds determine shape
Carbon bonding
o electron configuration allows covalent compatibility with many different elements
o most frequent partners hydrogen, oxygen, nitrogen
Molecular diversity - carbon skeleton
o skeletons vary
straight, branched, rings
length
double bonds - number, location
o change carbon skeleton, change the shape (structure)
Hydrocarbons
o organic molecules consist of only carbon and hydrogen
lipids or fats
hydrophobic
o petroleum - fossil fuel
partially decomposed remains of organisms millions of years ago
o can undergo reactions that release a large amount of energy
body stores fat
Carbon diversity
o isomers
compounds with same molecular formula but different structures and properties
structural
o have different covalent arrangements of their atoms or location of
double bond
geometric
o have the same covalent arrangements, but differ in spatial arrangements
inflexibility of double bonds
enantiomers
o isomers that are mirror images of each other
asymmetric carbon - attached to 4 different atoms (or groups
of atoms)
can be arranged in 2 different ways
one biologically active, other inactive
o pharmaceuticals
not equally effective
L-dopa - Parkinson's Disease
D-dopa - not effective
harmful - thaliomide 50-60's
o mixture of enantiomers - pregnant women
o reduced morning sickness
o severe birth defects
STRUCTURE IS IMPORTANT
o

Functional Groups
o chemical groups that affect molecular function
contribute by affecting molecules' shape
directly involved in chemical reactions
o each functional group participate in chemical rxn's in a characteristic way
o Functional groups:
Hydroxyl group : OH Name: Alcohols (names usually end in -ol)
Functional properties:
o Polar - result of the electronegative oxygen atom drawing electrons
toward itself
o Attracts water molecules, helping dissolve organic compounds
Hydrogen atom bonded to an oxygen atom, which is bonded to the carbon
skeleton
Carbonyl group : CO
Names: Ketone - carbonyl group is within a carbon skeleton | Aldehyde carbonyl group is at the end of the carbon skeleton
Functional properties:
o may be structural isomers with different properties. found in sugars.
Carbon double bonded to Oxygen
Carboxyl group : -COOH
Name: Carboxylic Acids (Organic acids)
Functional properties:
o Acidic properties - source of H+
Covalent bond between O and H so polar that H+ dissociates reversibly
Carbonyl group and a hydroxyl group
Amino group : -NH2
Name: Amines
Functional properties:
o Acts as a base; can pick up a H+ from the surrounding solution
o amine and a carboxylic acid (compounds with both groups are called
amino acids)
Sulfhydryl group : -SH (may be written HS-)
Name: Thiols
Functional properties:
o 2 sulfhydryl groups can interact to help stabilize protein structure
Phosphate group : -OPO32 Name: Organic phosphates
Functional properties:
o makes the molecule an anion negative charge
o potential to react with H2O, release energy
Reactive functional groups
Hydrophilic - increase solubility of organic compounds in water
Adenosine triphosphate (ATP)
o Organic phosphate molecule energy source
o Adenosine attached to 3 phosphate groups
Methyl group : -CH3- Not reactive, contributes to function by affecting shape
Name: methylated compounds
Functional properties:
o affects the expression of genes
transcription copy DNA into RNA

Translation "translate" RNA to protein

shape can change function
Sex hormones
only difference between estradiol (female) and
testosterone (male) is the functional groups

Basic concepts:
o carbon is the backbone of life
variation at the molecular level lies at the foundation of all biological diversity
o functional groups
be able to identify them
know their functions, characteristics
what groups are soluble in water? what groups are reactive?

END CHAPTER 4

Chapter 5: The Structure and Function of Biological Molecules

4 main classes of molecules

o carbohydrates
sugars and polymers of sugars
monomer monosaccharide, simple sugars (sweet)
disaccharide 2 sugars
o 2 monosaccharides joined by a glycosidic linkage
covalent bond formed by a dehydration rxn
lose a water --> building (bigger!)
o maltose = 2 glucose molecules
o sucrose = glucose + fructose (table sugar)
o lactose = glucose + galactose (milk)
polysaccharide many sugars linked
o macromolecules
o polymers of monosaccharides (monomers)
hundreds thousands of monomers
storage roles
storage polysaccharides
o starch storage polysaccharide of plands
consists entirely of glucose
monomers
granules within choloroplasts and
other plastids
o stored glucose major cellular fuel (energy)
o hydrolyze starch potatoes, wheat, corn
1-->4 linkage helical shape
o glycogen storage polysaccharide in
animals
mainly in liver and muscle cells

structural roles
structural polysaccharides
o cellulose major structural component of
plant cell walls
abundant organic compound on
earth
polymer of glucose, different
glycosidic linkages
o difference based on 2 ring structures of
glucose: alpha () & beta ()
o starch - -glucose helical shape
o cellulose - -glucose straight
H(+) on one strand H-bond with
OH(-) on other strands
parallel cellulose molecules
grouped into microfibrils, form
strong building materials for plants
o enzymes digest starch by hydrolyzing linkages | can't hydrolyze -linkages in
cellulose
o cellulose passes through the digestive tract
as insoluble fiber
abrade the wall, stimulating mucus
secretion
aids in the smooth passage of waste
o some microbes possess enzymes digest
cellulose
cows harbor bacteria rumen,
hydrolyze hay and grass
termites -- microbes to digest wood
symbiotic relationships
chitin exoskeleton of arthropods
and cell walls of many fungi
chitin can be used as surgical
thread
o ***COMPLEX CARBS***
o the structure and function of a polysaccharide are determined by:
sugar monomers
positions of glycosidic linkages
monosaccharide multiple unit of CH2O
glucose (C6H12O6) most common monosaccharide
monosaccharides classified by
o location of carbonyl group
aldose aldehyde sugar
end carbonyl group
ketose ketone sugar
middle carbonyl group
o structural isomers
glucose aldose

hydrolyze glycogen sugar demand

increases

lipids

fructose - ketose
number of carbons in carbon skeleton
number of carbons in skeleton
3-7 carbons long
drawn as linear skeleton, in aqueous solutions they form rings
triose 3 carbon ring
pentose 5 carbon ring
hexose 6 carbon ring
Glucose energy
monosaccharides major fuel for cells and raw material for
building molecules
cellular respiration extract energy from glucose (make ATP)
rapid absorption in body-insulin spike

do not form polymers

hydrophobic no affinity for water
consist mostly of hydrocarbons
nonpolar covalent bonds
some polar regions
most biologically important lipids:
fats
o not polymers, but are large molecules
assembled from smaller molecules
dehydration reactions
o constructed from 2 types of smaller molecules
glycerol
3 carbon alcohol (hydroxyl group attached to each
carbon)
fatty acids
carboxyl group attached to a long carbon skeleton
(16-18 atoms in length)
vary in length (number of carbons and number and
locations of double bonds)
saturated fatty acids
o maximum number of hydrogen atoms
possible and no double bonds
unsaturated fatty acids
o 1 or more double bonds
major function of fats
o energy storage
saturated fats
fats made from saturated fatty acids
o most animal fats are saturated
solid at room temperature
o TIGHTLY PACKED TOGETHER
BECAUSE NO DOUBLE BONDS
cardiovascular disease plaque deposits
Unsaturated fats
fats made from unsaturated fatty acids
plant and fish fats usually unsaturated
o "healthy fats"

liquid at room temperature oils

double bonds removal of hydrogen atom
o Cis double bond kink
Partially hydrogenated
o take unsaturated fat and remove double
bonds
o add hydrogens hydrogenate
o peanut butter, margarine prevents lipids
from spreading out
o unsaturated fats trans double bonds
trans fats
greater health concern than natural
saturated fats
o 3 fatty acids join to glycerol by an ester linkage, creating a
triacylglycerol (triglyceride)
o Ester linkage bond between hydroxyl group and carboxyl group
o Fats function energy storage
gram of fat, twice as much energy as a gram of sugar
(polysaccharide)
plants immobile, bulky storage starch granules
animals carry their energy stores around compact
long term storage adipose cells
protect vital organs
insulation marine mammals
phospholipids
o 2 fatty acids and a phosphate group attached to glycerol
o fatty acid tails hydrophobic
o phosphate group and attachments form a hydrophilic head (polar)
o added to water self-assemble into bilayer
hydrophobic tails pointing toward the interior
polar heads exterior
cell membranes
steroids
o carbon skeleton consisting of four fused rings
vary in their functional groups
o cholesterol, an important steroid, is a component in animal cell
membranes
o precursor to hormones (testosterone, estrogen, etc.)
inflammation
blood sugar
blood pressure
mineral balance
muscle mass

proteins
monomer amino acid
polymer polypeptides (chains of amino acids)
linked by peptide bonds
proteins are complex
consist of one or more polypeptides
TYPES OF PROTEINS:
enzymatic proteins

function:
selective acceleration of chemical reactions
o examples:
digestive enzymes (hydrolyze polymers in food)
structural proteins
o function:
support
o examples:
silk fibers (cocoons and spider webs), collagen and elastin
(animal connective tissues), keratin (hair, horns, feathers)
storage proteins
o function:
storage of amino acids
o examples:
ovalbumin (egg whites), casein (milk), storage proteins in
seeds
transport proteins
o function:
transport of other substances
o examples:
hemoglobin (blood), proteins that transport molecules across
cell membranes
hormonal proteins
o function:
coordination of an organism's activities
o examples:
insulin (helps regulate concentration of sugar in blood)
receptor proteins
o function:
response of cell to chemical stimuli
o example:
nerve cell receptors (detect chemical signals released b y other
nerve cells)
contractile and motor proteins
o function:
movement
o example:
actin and myosin (muscles), proteins responsible for
undulations of cilia and flagella
defensive proteins
o function:
protection against disease
o example:
antibodies (combat bacteria and viruses)
o

enzymes
protein catalyst
o speeds up chemical reactions
perform their functions repeatedly
enzymes very specific
amino acids (20)
organic molecule with carboxyl and amino groups

amino acids differ in their properties due to differing side chains (R groups)
****************AMINO ACIDS ARE CLASSIFIED ACCORDING TO
THEIR SIDE GROUPS ONLY********************
o nonpolar amino acids hydrophobic
o polar amino acids hydrophilic
o electrically charged amino acids
Polypeptides
unique linear sequence of amino acids
o range in length from few amino acids to more than a thousand
amino acids linked by peptide bonds
o join by dehydration rxn water removal
CARBOXYL TO AMINO IN BACKBONE
4 levels of Protein Structure
primary structure
o sequence of amino acids
AA sequence is like the order of letters in a long word
determined by inherited genetic information
between amino acids
covalent bond (peptide)
joined between amino and carboxyl group in backbone
secondary structure
o coils and folds in the polypeptide chain due to H-bonds in backbone
coils and folds result from H-bonds between polypeptide
backbone
only hydrogen bonds
between groups in backbone
ALPHA helix and BETA pleated sheet
structures formed
tertiary structure
o interactions among various side chains (R groups)
determined by interactions between R groups
Disulfide bridges may reinforce the protein's conformation
stabilize protein structure
hydrogen bonds
ionic bonds
quaternary structure
o multiple polypeptide chains
results when 2 or more polypeptide chains from one
macromolecule
collagen
consists of 3 polypeptides coiled like a rope
hemoglobin
consisting of 4 polypeptides: 2 ALPHA and 2 BETA
chains
sickle-cell disease
o inherited blood disorder
results from single AA substitution in hemoglobin
Protein conformation (shape)
primary structure, physical, and chemical conditions
alternations in pH, salt concentration and temperature can cause a protein to
unravel (unfold)

denaturation
o loss of a protein's native conformation
Protein-folding problem
very hard to predict a protein's conformation from primary structure
proteins go through several stages on their way to a stable conformation
chaperonins
o proteins that assist the proper folding of other proteins
prevents outside influences affecting protein polypeptides
while they fold together
o nucleic acids
2 types of nucleic acids
deoxyribonucleic acid (DNA)
o DNA directs own replication
o DNA directs synthesis of messenger RNA (mRNA) and controls
protein synthesis
ribonucleic acid (RNA)
nucleotide
nucleoside = side of nucleotide
nitrogenous base
o 2 types of nitrogenous bases
pyrimidines
6-membered ring
Cytosine
Thymine
Uracil
purines
6-membered ring to 5-membered ring
Adenine
Guanine
pentose sugar
o 5 carbons
o (ribose sugar)
phosphate group
macromolecules (form polymers chains)
carbohydrates
proteins
nucleic acids
o large molecules composed of thousands of covalently connected atoms
o polymers chain-like molecules
long molecules consisting of identical building blocks linked by covalent bonds
o monomers repeating unit ("building block")
Differs in:
o how they are built
o structure and function
unique properties arise from orderly arrangement of atoms
SYNTHESIS AND BREAKDOWN OF POLYMERS:
o Each class different monomer
o build polymer dehydration rxn (condensation rxn)
lose a H2O molecule
dehydration rxn
synthesis of a polymer

removes water molecule, forms new bond

one monomer provides H+, the other OH facilitated by enzymes (proteins that speed up the chemical rxn in cells)
o break down polymer hydrolysis rxn
add a H2O molecule
hydrolysis
breakdown of a polymer
hydrolysis adds water molecule, breaks a bond
digestive system
o enzymes break down food
Diversity of polymers
o each cell has thousands of different macromolecules
o an immense variety of polymers can be built from a small set of monomers
26 letters in alphabet thousands of words
20 amino acids thousands of proteins
Nucleotide polymers
o nucleotides joined by covalent bonds that form between the OH group on the 3' Carbon of 1
nucleotide and the phosphate on the 5' carbon on the next
phosphodiester bond
o creates a backbone of sugar-phosphate units with nitrogenous bases
o DNA sequence is unique for each gene
genes encode proteins
1 DNA molecule includes many genes
23 pairs of chromosomes
DNA Double Helix
o 2 polynucleotides in helix
o 2 backbones run in opposite 5' to 3' directions from each other
antiparallel
o nitrogenous bases in DNA form hydrogen bonds:
A always with T (U-RNA) 2 bonds
G always with C 3 bonds
PYMIRIDINE 1 RING; 3 TOTAL
YOU WANT TO EAT PIE, CUT IT
o C-U-T --> PYRMIRIDINE
*******COMPLIMENTARY BASE PAIRING*********

Carbohydrate
Lipids
Proteins
Structure
Primary
Secondary
Tertiary
Quaternary

Glycosidic linkage
Ester Bond
Peptide bond

Monosaccharide

Polysaccharide

Amino acid

Polypeptide

Bonds
Covalent peptide bonds
Hydrogen bonds
All types of bonds
All types of bonds

Between
Amino acids
AA backbone
AA side groups
polypeptides

END CHAPTER 5

Chapter 6: A Tour of the Cell

The importance of cells

o All organisms are made of cells
o The cell is the simplest unit of life
o Cell structure is correlated to cellular function
o All cells are related by their descent from earlier cells
o Fundamental themes in biology
Structure = function
Cells respond to their environment
Microcopy
o Discovery of microscope in 16th century enabled us to study cells and their components
o Light microscope use visible light to magnify an image
Passes light through a specimen and then through glass lenses
Lenses refract (bend) light, magnifying the image
o Light microscopy
Magnification ratio of an objects image size to its real size
Multiple objective lens (4x) times ocular lens (10x) = 40x
Resolution measure of the clarity of the image

Minimum distance 2 points can be separated and still be distinguished as 2

points
Shorter wavelength better resolution
Minimum resolution ~200 nanometers (nm)
Magnify effectively to ~1000 times the size of the actual specimen
Various techniques enhance contrast and enable cell components to be stained
Most cellular organelles too small to be resolved
o Electron microscopy
Scanning electron microscopes (SEMs) focus a beam of electrons onto the surface of a
specimen
Provides 3D image
Transmission electron microscopes (TEMs) focus a beam of electrons through a
specimen
Mainly to study the internal ultrastructure of cells
Electrons shorter wavelength than visible light better resolution (clarity)
Resolution 2nm
Cell classification
o Classifying cells
Domains
Bacteria
Archaea
o Prokaryotes
Eukaryote
o Eukaryotes
Kingdoms
Eubacteria
Archaebacterial
o Bacteria, cyanobacteria
Plantae
Animalia
Protists
Fungi
Prokaryotic and eukaryotic cells
Basic features of all cells
o Plasma membrane
o Cytosol
Fluid inside cell
o Genetic information
o Ribosomes
Make proteins
Cytoplasm
o Interior of cell
Used interchangeably with cytosol
Prokaryotes:
o No nucleus
o Cell wall
Plant cell walls cellulose
Fungi cell walls chitin
o No membrane-bound organelles
o Smaller
o Simple

Eukaryotes:
o Nucleus
o No cell wall
ANIMAL CELLS ONLY
o Membrane-bound
o Larger
o complex

Cell size
o Logistics of carrying out cellular metabolism sets limits on the size of cells
o Needs a certain level of metabolic ability to support all reactions taking place inside
Large cell high level of metabolism
Small cell lower level of metabolism
o CELL CAN ONLY GROW TO THE EXTENT THAT IT CAN SUPPORT ITSELF
o Increase size increase volume and surface area
o Volume increases more than surface area
Smaller object has a greater surface-to-volume ratio than a larger object
High surface-to-volume, facilitate exchange of materials between cells and its
environment
o Area calculated in square units (l x w)
o Volume calculated in cubic units (l x w x h)
Cell organelles
o Plasma membrane
Selective barrier that allows sufficient passage of oxygen, nutrients, waste, to service the
volume of the cell
For each square m of membrane, only so much of a particular substance can cross per
second
Rates of chemical exchange with the environment could be inadequate to maintain a large
cell
Surface area must be sufficiently large to accommodate volume explains microscopic
size
LARGE ORGANISMS DO NOT HAVE LARGER CELLS, THEY HAVE MORE
CELLS --- duh -- Function
Exchange material with surroundings, need a lot of surface area
o Intestinal epithelial cell microvilli
o Long thin projections
o Increase surface area, not volume
Biological membrane is a double layer of phospholipids
Each membrane has a unique composition of lipids and proteins suited to that
membranes functions
o Nucleus
Nucleus contains DNA
Some genes mitochondria and chloroplast
Nuclear envelope encloses the nucleus, separating it from the cytoplasm
Double membrane (phospholipid bilayer)
Pores
Protein pore complex lines each pore, regulating entry and exit of
macromolecules
Nuclear lamina
Lines inside of the nuclear membrane
o Netlike array of protein filaments maintains the shape

Nuclear matrix
Framework of fibers extends throughout the nuclear interior
Chromosomes
DNA in discrete units
Human cell 46 chromosomes
Chromatin
Complex of proteins and DNA
Nucleolus
Ribosomal RNA (rRNA) is synthesized
rRNA is assembled into large and small subunits
Ribosomes
Make proteins using DNA as directions
Made of rRNA and protein
Ribosomes carry out protein synthesis in two locations:
o In the cytosol free ribosomes
o On the outside of the endoplasmic reticulum (ER) bound ribosomes
Bound ribosomes
o Make proteins found in membranes, packaged within organelles,
exported (secreted)
Free ribosomes
o Make proteins found in cytosol
Endomembrane system
Components of the endomembrane system:
Nuclear envelope
Endoplasmic reticulum
Golgi apparatus
Lysosomes
Vacuoles
Plasma membrane
NOT IDENTICAL IN STRUCTURE OR FUNCTION
Components are either continuous or connected via transfer by vesicles
Endomembane system functions
Synthesize proteins
Transport proteins into membranes/organelles
Transport proteins out of cell
Metabolism and movement of lipids
Detoxification of poisons
Endoplasmic reticulum
Accounts for more than the total membrane in many eukaryotic cells
Consists of tubules and sacs cisternae
There are two distinct regions of ER:
o Smooth ER, which lacks ribosomes
o Rough ER, with ribosomes
ER membrane is continuous with the nuclear envelope
ER lumen (cisternal space)
Smooth ER
o Lacks ribosomes
o Synthesizes lipids
Phospholipids
Steroids

o
o
o

o
o

Sex hormones
o Testes/ovaries lots of smooth ER
Metabolizes carbohydrates
Stores calcium muscles
Detoxifies drugs liver
Makes more soluble secrete
add a hydroxyl group
Drink a lot increase smooth ER in liver cells- speed up
rate of detox- tolerance
Muscle contracts based on concentration of Ca crossing membranegenerates nerve impulse
Membrane potential

o
Rough ER
Bound ribosomes
Produces secreted proteins
o Hormone insulin from pancreas cells
Polypeptide chain goes into ER lumen through a pore in ER membrane
o Folded into native conformation
o Secreted proteins glycoproteins
o Protein covalently bonded to a carbohydrate
Secretory proteins distributed by transport vesicles
o Depart ER wrapped in membranes from transitional ER
o Transport vesicles vesicles moving from one area of cell to another
Makes membranes
Polypeptide grows from ribosome, inserted into ER membrane
o Anchored by hydrophobic portions
o Transferred in transport vehicles
Golgi apparatus
Products of ER modified and stored, sent out
Cells involved in secretion lots of golgi
Flattened membrane sacs cisternae
Polar membrane (2 different sides)
o Differ in thickness and molecular composition
o Cis face receives vesicles from ER
o Trans face sends vesicles out to other sites in cell
Proteins are modified as they move cis to trans membranes
o Glycoproteins carbohydrates get modified
Manufactures certain macromolecules
o Polysaccharides (carbohydrates)
Sorts vesicles for various parts of the cell
o Molecular tag phosphate group
o External receptor recognizes docking site on specific organelle
Lysosomes
Membrane sac holds hydrolytic enzymes
o Breakdowns proteins, fats, carbs, nucleic acids
Proteins in the inner surface of the membrane or enzymes themselves 3D
conformations protect vulnerable bonds form enzymatic attack
Acidic environment
Engulf smaller organisms or food particles (amoebas)
o Phagocytosis
o Breaks down into monomers simple sugars, amino acids

o Pass into cytosol as nutrients for the cell

o Macrophage immune cell, ingests microorganisms
Autophagy recycle organelles and macromolecules
o Membranes fuse
o Enzymes break it down
o Returns to cytosol for reuse
Liver cell recycles half its macromolecules each week
Tay-Sachs Disease
o Genetic mutation (autosomal recessive) rare
o Lack hydrolytic enzymes to break down lipids
o Build up in lysosome, interfere with other cellular activities
o Brain becomes impaired by accumulation of lipids
o Cherry red spot on back of retina
o Infantile- die by age 5, blind, deaf, cant swallow, paralysis set in
o Juvenile ages 2-10, dead by 5-15 yrs old,
o adult/late onset- nonfatal- neurological deterioration, unsteady gait,
paralyzed, mental illness shizofren
Vacuoles
Large vesicles membrane-bound sacs
Food vacuole formed by phagocytosis, fuses with lysosome
Contractile vacuole pump excess water out of a cell to maintain the salt
concentration, protists
Central vacuole plants, enclosed by tonoplast (membrane)
o Organic molecules
o Inorganic ions potassium and chloride
o Disposal sites metabolic by-products
o Pigments color flower petals
o Store water
Plant cell central vacuole
o Plant growth cell enlarge as vacuole absorb water
o Cell became larger with minimal investment in new cytoplasm
o Cytosol occupies thin layer between plasma membrane and tonoplast
o Ratio of membrane surface to cytosolic membrane is great, even for a
large cell
CONCLUDES ENDOMEMBRANE SYSTEM
Mitochondria
Sites of cellular respiration
Respiration metabolic process generates ATP by extracting energy from sugars and fats
using oxygen.
Membrane-bound organelle membrane not made by rough ER
Made by free ribosomes in cytosol
Ribosomes within itself and DNA
Cells can have hundreds to thousands of mitochondria
More active cells have more mitochondria
Smooth outer membrane and inner membrane folded into cristae each is a phospholipid
bilayer
Inner membrane creates two compartments:
Intermembrane space
Mitochondrial matrix
o Contains
Enzymes

Mitochondrial DNA
Ribosomes
Metabolic steps of cellular respiration are catalyzed in the mitochondrial matrix
Cristae present a large surface area for enzymes that synthesize ATP, increasing
productivity of respiration
MITOCHONDRIA = POWERHOUSE OF THE CELL
Chloroplasts
Type of organelle called a plastid
Only in plants and algae contain the green pigment chlorophyll and enzymes that
function in photosynthesis
In leaves and other green organs of plants and in algae
Convert solar energy to chemical energy by absorbing sunlight and using it to drive the
synthesis of organic compounds, like sugars from CO2 and H2O
Thylakoids membranous sacs
Granum stack of thylakoids
Stroma internal fluid
Contain ribosomes and DNA
Divided into 3 compartments
Intermembrane space
Stroma
Thylakoid space
Replicate themselves
Mobile and move within the cell
Peroxisomes
Specialized metabolic compartments bounded by a single membrane
Produce hydrogen peroxide and converts it to water
Enzymes that transfer hydrogen from substances to oxygen
Special enzymes (peroxidase) converts H2O2 to O2
Use oxygen to break down fatty acids fuel in mitochondria
Liver detoxify alcohol and drugs
Cytoskeleton
Network of fibers extending throughout the cytoplasm
Composed of 3 types of molecular structures
Microtubules thickest
o Hollow rods tubulin
Tubulin dimer
Alpha and Beta subunits
o Grow in length add a dimer
Disassembled as well
o Plus side accumulates/releases dimers at a higher rate
o Function:
Maintain cell shape
Cell motility
Separate chromosome division
Organelle movement
o Centrosomes and Centrioles
In animal cells microtubules grow out from a centrosome
(MTOC)
Region near the nucleus, microtubule-organizing
center

Centrioles within centrosome, each with 9 triplets of

microtubules arranged in a ring
Centrosome
Space in cell where centrioles grow out of
o Cilia and Flagella
Microtubules control the beating of cilia and flagella
Cilia and flagella differ in their beating patterns
A core of microtubules sheathed by the plasma membrane
Basal body anchors the cilium or flagellum
9+2 pattern
9 doublets in a ring
2 single in the center
Dynein motor protein drives the bending movements
Located on outer doublet in pairs
Reach toward neighboring doublet
Pairs are like feet
One foot maintains contact on microtubule
Other foot releases and reattaches further along
Protein cross-linking between microtubules
Limits dynein feet from walking too far
Microfilaments (actin filaments) thinnest
o Solid rods actin
Twisted double strand of actin subunits
o Linear filaments and networks
Inside plasma membrane cortical microfilaments
Cortex outer cytoplasmic layer (gel)
o Functions:
Maintain cell shape
Muscle contraction
Cell motility pseudopodia
Cell division cleavage furrow
o Actin filaments muscle
Thousands of strands of actin parallel with thicker filaments
myosin
Myosin walks along actin
Contraction actin and myosin sliding past each other
Intermediate filaments middle
o Diverse class of cytoskeletal fibers
o Made out of keratin proteins
o Permanent fixture dont disassemble
o Functions:
Cell shape
Organelle positioning
Make up nuclear lamina

Roles:

Support cell and maintain its shape

o Animal cells lack cell walls
Remarkable strength and resilience
o Stabilized by balance of opposing forces
Provides anchorage for organelles
Dynamic quickly dismantled and reassembled

Motility cell movement and parts within the cell

Motor proteins bind tubules, filaments
o Slide them past one another
o Similar to how muscles contract
Vesicles, organelles travel along microtubules
o Neurotransmitter molecules migrate to tips of axons
o ER transport vesicles travel to Golgi
Manipulate plasma membrane to form vesicles
Extracellular components
Cell walls of plants
o Extracellular structure in plant cells
NOT IN ANIMAL CELLS
o Functions:
Protects the plant cell, maintains its shape, prevents excessive
uptake of water
o Made of cellulose fibers secreted and embedded in matrix of
polysaccharides and proteins
o Multiple layers:
Primary cell wall
Relatively thin and flexible
Middle lamella
Thin layer between primary walls of adjacent cells
o Rich in pectins (polysaccharides)
Secondary cell wall
In some cells; added between the plasma membrane
and the primary cell wall
o Strengthen the wall, offers protection
Plasmodesmata
Channels between adjacent plant cells
Extracellular matrix (ECM)
o Extracellular structure in animal cells
o Made of glycoproteins
Most abundant collagen
o Embedded in proteoglycan network
Small core protein with many carbohydrate chains covalently
attached
o Cells attach to ECM by fibronectin (glycoprotein)
Integrins on cell surface bind fibronectin and microfilaments
on the inside (cytoplasm)
o CFIM - order
o Functions:
Support
Adhesion
Movement
Tissue regeneration
Intercellular junctions
o Neighboring cells in tissues, organs
Adhere, interact, and communicate through direct physical
contact
o Intercellular junctions facilitate this contact
o Plant cells plasmodesmata

Plasma membranes of adjacent cells line plasmodesmata

Cytosol passes through and connects the chemical
environments of adjacent cells (water, macromolecules)
Unify most of plant into one living continuum
Animal cells
Tight junctions
Membranes of neighboring cells are pressed together,
preventing leaking of extracellular fluid
Desmosomes
(anchoring junctions)
o Fasten cells together into strong sheets
Gap junctions
Provide cytoplasmic channels between adjacent cells
ALL 3 COMMON IN EPITHELIAL TISSUE LINES
EXTERNAL AND INTERNAL BODY SURFACES

END CHAPTER 6

Chapter 7: Membrane Structure and Function

Key Concepts
o Membrane composition
o Membrane fluidity
fatty acids, cholesterol
o Membrane proteins
o Membrane permeability
diffusion, osmosis, tonicity, osmoregulation
active transport, membrane potential
Plasma membrane
o Boundary that separates living cells from its environment
o Selective permeability
allowing some substances to cross it more easily than others
Cellular membranes
o Composed of lipids, proteins, carbohydrates
phospholipids
most abundant lipid in the plasma membrane
o Amphipathic molecules
containing hydrophobic and hydrophilic regions
Fluid mosaic model
o Membrane is a fluid structure with a 'mosaic' of various proteins embedded in it

Hydrophilic region
of protein
Phospholipid
bilayer
Hydrophobic region of protein

Fluidity of membranes
o phospholipids in the plasma membrane can move within the bilayer (fluid like salad oil)
held in place by hydrophobic interactions (weak)
o lipids, (some proteins), drift laterally
o rarely molecule flip-flop across the membrane

Lateral movement
Flip-flop
(~107 times (~
per
second)
once
per month)
As temperatures cool, membranes switch from a fluid to solid state (losing kinetic energy)
Temperature where membrane solidifies depends on types of lipids (fatty acids)
MEMBRANES RICH IN UNSATURATED FATTY ACIDS ARE MORE FLUID AT LOWER
TEMPERATURE THAN SATURATED FATTY ACIDS
(As temperature decreases, animal/plant would want to increase unsaturated fatty acids)
o MORE UNSATURATED FATS = MORE FLUID MEMBRANE
o MORE SATURATED FATS = LESs FLUID MEMBRANE
o When temperature begins to decrease
more unsaturated fats = will not freeze
Cholesterol
o Cholesterol (steroid)
effects membrane fluidity depending on the temperature
o warm temperatures restrains movement of phospholipids, making them less fluid
o cool temperatures maintains fluidity by preventing tight packing
lowers the temperature required for a membrane to solidify
o
o
o

CHOLESTEROL IN ANIMAL CELL MEMBRANE; FLUIDITY MUST BE MAINTAINED TO WORK

PROPERLY; BALANCED. TOO FLUID OR NOT FLUID ENOUGH WILL CAUSE CELL TO NOT FUNCTION

Membrane proteins
o proteins in the plasma membrane can move
o different types of cells have different types of proteins in their plasma membrane
o integral protein
penetrate the hydrophobic core of the lipid bilayer
transmembrane protein spans the entire membrane
o peripheral protein
not embedded in the membrane, bound to it
o 6 major functions of membrane proteins
TRANSPORT
hydrophilic channel or ATP to actively pump substance across
ENZYMATIC ACTIVITY
help transport substances across membrane
SIGNAL TRANSDUCTION
communication with environment
CELL-CELL RECOGNITION
communication with other cells
cells recognize each other by binding to surface molecules
recognize self vs non-self (pathogens, transplant tissue)
surface molecules usually carbohydrates
o covalently bonded to lipids glycolipids
o covalently bonded to proteins glycoproteins
markers on your blood cells
o type A, B, AB, or O
INTERCELLULAR JOINING
tight junctions
ATTACHMENT TO THE CYTOSKELETON AND ECM
attachment to cytoskeleton or ECM
Taking Every Single Call Is Annoying

Permeability of the Lipid Bilayer

o Hydrophobic (nonpolar) molecules dissolve in the lipid bilayer and pass through the membrane
rapidly
gases, very small
hydrocarbons nonpolar
o Hydrophilic (polar) molecules do not cross the membrane easily
sugars (glucose), ions, water
cross through membrane proteins
Transport proteins

allow passage of hydrophilic substances very specific

channel proteins hydrophilic channel that specific molecules or ions can use as a tunnel
aquaporins facilitate the passage of water
o carrier proteins bind to molecules and change shape to shuttle them across the membrane
Types of transport
o passive (diffusion): high to low
channel proteins
aquaporin or ion channel
carrier proteins
o active: low to high
ONLY carrier proteins
o
o

HYDROPHOBIC SUBSTANCES DIFFUSE RIGHT ACROSS MEMBRANE. DO NOT NEED

TRANSPORT PROTEINS.

d
Thermal motion (heat)

movement of molecules
o Diffusion
molecules spread out evenly into the available space
each molecule moves randomly (Brownian motion)
all of the molecules movement in one direction
o Molecules move HIGH concentration to LOW concentration
equally spread throughout
Factors that affect diffusion
o Heat
increase heat, increase molecular collisions, increase diffusion rate
direct relationship
o Size
smaller molecules move faster than larger molecules, smaller molecule will diffuse faster
inverse relationship
o Concentration gradient
steeper gradient, faster diffusion
direct relationship
DIFFUSION IS A SPONTANEOUS PROCESS; NO WORK DONE, NO ENERGY ADDED TO THE
SYSTEM - PASSIVE
Concentration gradient
o the difference in concentration of a substance from one area to another
MOVES HIGH TO LOW
Passive transport
o requires no energy from the cell to occur
SPONTANEOUS
Only happens in a cell if the substance can readily cross the plasma membrane
Water can diffuse across the cell membrane through aquaporins (hydrophilic channels) facilitated
diffusion
DIFFUSION REFERS TO THE MOVEMENT OF SOLUTE (MOLECULES) DOWN ITS OWN
CONCENTRATION GRADIENT
OSMOSIS IS THE DIFFUSION OF WATER; SOLUTION
Osmosis
o diffusion of water across a selectively permeable membrane
Water is diffusion on its own concentration gradient
o from a high to low concentration
o

Water diffuses across a membrane

o from an area of low solute concentration (high water concentration) to an area of high solute
concentration (low water concentration)
Tonicity
o ability of a solution to cause a cell to gain or lose water
Isotonic solution
o solute concentration is the same as that inside the cell; no net water movement across the plasma
membrane
o extracellular solution = intracellular solution
Hypertonic solution
o solute concentration is greater than that inside the cell; cell loses water (cell shrivels up)
o extracellular solution > intracellular solution
Hypotonic solution
o solute concentration is less than that inside of the cell; cell gains water (cell burst)
o extracellular solution < intracellular solution
Osmoregulation
o water balance
o cells use to maintain internal environment
o controls the balance of water within themselves and the outside environment
o Paramecium lives in a hypotonic environment (pond water)
contractile vacuole that acts as a pump
WATER BALANCE WITH CELL WALLS
o Hypotonic environment
plant cell swells, cell wall exerts pressure, opposes uptake turgid (firm)
o Isotonic environment
no net movement of water; flaccid (wilt)
o hypertonic environment
plant cells lose water
plasmolysis plasma membrane pulls away from the wall
o PLANTS, BACTERIA, FUNGI
TONICITY AND OSMOREGULATION
o Tonicity
ability of a solution to cause a cell to gain or lose water
o Osmoregulation
animals/plants control the balance of water within themselves and the outside
environment
FACILITATED DIFFUSION
o Passive diffusion aided by transport proteins
o transport proteins speed movement of polar molecules across the plasma membrane
very specific, water or small ions
o channel proteins
provide corridors that allow a specific molecule or ion to cross the membrane
o ion channels
gated channels, stimulus causes them to open/close
stimulus
o chemical or electrical
chemical
o not the substance that will be transported
neutrotransmitter can open Na+ ion channels
o carrier proteins
undergo change in shape that translocates the solute-binding site across the membrane

ACTIVE TRANSPORT
MOVES SOLUTES AGAINST THEIR GRADIENTS
REQUIRES ENERGY, USUALLY ATP
Performed by carrier proteins only
channels are just open passage ways diffusion only
solution-potassium pump
higher concentration of K+ and lower concentration of Na+ inside the cell
compared to environment
maintains concentration gradients of sodium and potassium across cell
membranes
o Pumps 3 Na+ OUT of cell
o Pumps 2 K+ INTO cell
Cell basics
o INSIDE OF CELL IS NEGATIVE
o INSIDE OF CELL HAS LOW SODIUM (NA+)
o INSIDE OF CELL HAS HIGH POTASSIUM (K+)
o IF NA+ CHANNELS ARE OPENED, NA+ DIFFUSES INTO THE CELL
o IF K+ CHANNELS ARE OPENED, K+ DIFFUSES OUT OF THE CELL
o **************THINK OF CONCENTRATION GRADIENT AS AN ENERGY
SOURCE************
Maintenance of Membrane Potential
o All cells have voltage across their plasma membranes
Voltage
electrical potential energy, separation of opposite charges
o Cytoplasm has a negative charge compared to extracellular fluid
unequal distribution of anions and cations
o membrane potential
voltage difference across a membrane
range
-50 to -200 mV
o minus sign indicated negative inside the cell compared to outside
acts like a battery
energy source that affects the trafficking of all charged substances across the
membrane
inside cell is negative
membrane potential favors the passive transport of cations into the cell and
anions out of the cell.
Electrochemical gradient
o two combined forces drive the diffusion of ions across a membrane
ion's concentration gradient chemical force
effect of the membrane potential on the ion's movement electrical force
o passive diffusion
ion moves "down" its electrochemical gradient
includes concentration, as well as charge across membrane
o Electro- = charge
o chemical = concentration gradient
o SPECIFIC FOR IONS BECAUSE THEY HAVE A CHARGE
Electrogenic pump
o membrane proteins contribute to membrane potential (difference of voltage across the membrane)
Sodium-potassium pump
o pumps 3 Na+ ions for every 2 K+ ions pumped in
o

net transfer of +1 charge to extracellular environment

stores energy in form of voltage
o electrogenic pump transport protein that generates the voltage across a membrane
-genic = generates
electro- = charge
PUMPS ESTABLISH CONCENTRATION GRADIENTS; SET CHARGE DIFFERENCE
o NEED ATP; ACTIVE TRANSPORT
Cotransport
o coupled transport
o occurs when active transport of a solute indirectly drives transport of another solute
o cotransporter protein (separate from the pump)
couples the "downhill" diffusion of one substance to the "uphill" transport f a 2nd
substance
passive process
o AKA SECONDARY ACTIVE TRANSPORT
sometimes referred to as "secondary active transport"
Antiporters opposite directions, symporters same direction
o ONE OF TRANSPORTED MOLECULE HAS TO BE HYDROGEN
o SUCROSE GOES FROM HIGH TO LOW; GOES AGAINST GRADIENT
o ENERGY SOURCE = HYDROGEN ION GRADIENT
o TRANSPORTER WON'T FUNCTION WITHOUT PUMP TO SET UP GRADIENT
Bulk transport
o large molecules cross the membrane via vesicles
o exocytosis
transport vesicles migrate to membrane, fuse with it, and release their contents
many secretory cells use exocytosis to export their products
EXO = EXIT
o endocytosis
cells take in macromolecules by forming vesicles from the plasma membrane
reversal of exocytosis, involving different proteins
3 types
phagocytosis (eating)
o cell engulfs particles in a vacuole
pinocytosis (drinking)
o cell creates vesicle around fluid
receptor-mediated endocytosis
o binding of ligands to receptors triggers vesicle formation
ENDO = ENTER
TRANSPORT ACROSS MEMBRANE RECAP
o Passive no energy; HIGH TO LOW
diffusion across membrane
small or hydrophobic (nonpolar) molecules only
facilitated diffusion (through a transport protein)
channel protein specific, some "gated"
carrier protein specific
o Active energy (ATP); LOW TO HIGH
molecule must go through transport protein
carrier proteins only
o PUMP ACTIVE
o ATP ACTIVE
o DIFFUSION PASSIVE

END CHAPTER 7

Chapter 8: An Introduction to Metabolism

What is metabolism?
o All the chemical reactions in an organism
Metabole change
o Metabolism manages the matter and energy resources in a cell
o Thousands of chemical reactions occurring in any cell at one time
o These reactions intersect into metabolic pathways
Metabolic pathways
o begins with a specific molecule, it is altered in a series of steps, resulting in a specific product
o each step is catalyzed by a specific enzyme
o enzymes are not consumed
o substrate what enzyme picks up
specific
Metabolic enzymes
o mechanisms that regulate enzymes catalyzing the metabolic pathway
o these balance supply and demand
o avert deficits or surpluses of cellular molecules
Metabolism
o catabolic pathways
release energy
break down complex molecules into simpler compounds
cellular respiration breaks down glucose
catabolism "downhill"
CATAPULT BREAK DOWN WALLS ETC.
o anabolic pathways
consume energy
build complex molecules from simpler ones
protein synthesis from amino acids
anabolism "uphill"
Forms of energy
o energy
the capacity to cause change
some energy can perform work (rearrange matter)
o work
move matter against opposing forces (gravity)
examples: contract muscles, active transport
o exists in various forms
cells need to transform energy from one form to another to perform the functions of life
solar, thermal, chemical, electrical, mechanical
o kinetic energy
energy associated with motion
heat (thermal energy)
o energy associated with random movement of atoms or molecules

moving objects can perform work by transferring motion to other matter

pedal a bike, moving legs, billiards
o potential energy
energy that matter possesses because of its location or structure
chemical energy
o energy available for release in a chemical reaction
molecules store energy due to arrangement of their atoms
glucose is a high energy molecule
broken down into simpler molecules
o arrangement requires less energy, excess energy is released
The laws of energy transformation
o thermodynamics
study of energy transformations
system describes the matter under study
surroundings everything outside the system
o closed system
isolated from its surroundings
liquid in a THERMOS bottle
governs energy transformations
o open system
energy and matter can be transferred between the system and its surroundings
organisms absorb energy from surroundings and release heat and metabolic waste
products
governs energy transformations
First Law of Thermodynamics
o energy can be transferred and transformed, but it cannot be created nor destroyed
o principle of conservation of energy
energy of the universe is constant
Second law of thermodynamics
o Why cant we recycle our energy instead of eating?!
o Every time energy is transferred/transformed, most of it becomes unusable- unavailable to do
work
We lose it! Usually as heat (the energy associated with random motion of
atoms/molecules)
Small fraction of the food you eat is transformed into usable energy, most is lost as heat
to your surroundings.
The only use for heat in a living cell (temperature is uniform) is warming an organism.
Crowded room gets hot- lots of chemical rxns occurring!
o every energy transfer/transformation increases the entropy (disorder) of the universe
entropy measure of randomness or disorder
o there is an unstoppable trend toward randomization of the universe as a whole
o increased entropy
evident in the physical disintegration of systems organized structure
building falls apart unmaintained
room gets messy
increasing entropy in the universe less apparent
appears as increasing amounts of heat
less ordered forms of matter (less structured, more random)
Why do certain processes in biology occur "naturally"?
For a process to occur on its own, without input of energy, it must increase the entropy of the universe
o Breaking down or downhill reaction

Spontaneous process- no input of energy, i.e. water flows down hill

o HIGH TO LOW
Nonspontaneous process- cannot occur on its own, needs energy added to the system
o Water being pumped uphill
o LOW TO HIGH
BIOLOGICAL ORDER AND DISORDER
o Living systems increase the entropy of their surroundings
o Organisms break down ordered forms of matter and energy (release energy)
o Cells also create ordered structures from less ordered materials (input energy into system)
How can we tell which reactions occur spontaneously and which require input of energy?
o Determine chemical energy changes in chemical reactions
o Gibbs free energy of a system
measures the portion of a system's energy that can perform work when temperature and
pressure are uniform throughout the system (living cell)
Free energy change (DELTA G)
o DELTA = change
o free energy (G) = energy that can do work when temperature and pressure are uniform
o change in free energy (DELTA G) is related to the change in ENTHALPY (DELTA H) and change
in ENTROPY (DELTA S)
o Enthalpy
change in total energy (DELTA H)
o Entropy
measure of disorder (DELTA S)
o Total energy minus lost energy = energy available to do work
DELTA H DELTA S = DELTA G
o Every spontaneous process decreases that system's free energy
energy that can do work
water flows downhill, losing energy
DELTA G = G(FINAL) G(INITIAL)
spontaneous processes are negative
loss of energy (lost for that "system" BUT used elsewhere)
final state has LESS free energy, less likely to change, more stable
LESS FREE ENERGY = MORE STABILITY
o Only processes with a NEGATIVE DELTA G are spontaneous
DELTA G = POSITIVE OR ZERO, NEGATIVE SPONTANEOUS
o Spontaneous process
total energy (Enthalpy (H)) must decrease or
Disorder (entropy (S)) must increase
OR BOTH
Free energy, stability, and equilibrium
o free energy
measure of a system's instability
tendency to change to a more stable state
ENERGY FLOWS FROM HIGH TO LOW
o unless prevented, system will move towards greater stability (HIGH G TO A LOW G)
o during a spontaneous change, free enrgy decreases and the stability of a system increases
o EQUILIBRIUM
STATE OF MAXIMUM STABILITY
o System naturally move to equilibrium (STABLE STATE LOW ENERGY)
o system at equilibrium cannot spontaneously change it cna do no work (low free energy)

SPONTANEOUS PROCESS CAN ONLY PERFORM WORK WHEN IT IS MOVING TOWARD

EQUILIBRIUM
Free energy and metabolism
o endergonic
nonspontaneous, consumes energy (energy inward)
absorbs free energy from its surroundings
uphill reactions, low to high, anabolic
o exergonic
spontaneous, releases energy (energy outward)
downhill, high to low, catabolic
released energy is used in other reactions
Exergonic reactions
o Lose free energy, G decreases
o DELTA G IS NEGATIVE
o magnitude of DELTA G represents the maximum amount of work the reaction can perform
o greater the decrease in free energy, greater amount of work can be done
o SPONTANEOUS, CATABOLIC
o EXO ENERGY GOES OUT; RELEASED SO THAT IT CAN BE USED TO DO WORK
Endergonic reactions
o absorbs (consumes) free energy
"storing" free energy
o G increases, DELTA G IS POSITIVE
o nonspontaneous, anabolic
o magnitude of the DELTA G is the quantity of energy required to drive the reaction
o

Spontaneous

Nonspontaneous

Downhill

Uphill

Catabolic

Anabolic

Release energy

Consume energy

-G, -H, +S,

+G, +H, -S,

Exergonic

Endergonic

Equilibrium and metabolism

o reactions in a closed system eventually reach equilibrium and then do no work
o cells are not in equilibrium
open systems experiencing a constant flow of materials
o catabolic pathways in a cell releases free energy in a series of reactions
prevent reaching equilibrium, product does not accumulate

CANNOT MAKE AN ENDERGONIC RXN TURN INTO AN EXERGONIC RXN

COUPLED REACTION BECOMES EXERGONIC (TOTAL ENERGY)

Phosphate attach to another molecule; changes energy state of that molecule due to the increased negative charges of
the phosphate

Coupled reactions: overall DELTAG is negative; together, reactions are spontaneous

enzymes can catalyze exergonic reactions

increase reaction rate

exergonic rxns need to absorb small amount of energy from surroundings
endergonic rxns need to absorb energy from another system

exergonic negative deltag

activation energy
surrounding energy
EA
not usable for work
energy used for exergonic reaction to move forward

enzymes catalyze reactions by lowering activation energy

DELTAG is unaffected by enzyme

enzymes lower activiation energy

orienting substrates correctly proper contact
sraining substrate bonds transition from EA directly proportional to ajfadafjhakfsjh

catabolic pathways yield energy

complex organic compounds store energy

RELOCATION OF ELECTRONS
fermentation anaerobic respiration ( NO OXYGEN )
inefficient
partial degradation of sugars
cellular respiration
consumes oxygen (aerobic)
much more efficient than fermentation
TRANSFER OF ELECTRONS RELOCATION ELECTRONS RELEASES STORED ENERGY IN ORGANIC
MOLECULES
redox rxns
transfer of electrons from one reactant to another
OXIDATION LOSE ELECTRON
REDUCTION GAIN ELECTRON (BECOME MORE NEGATIVE)
ELECTRON DONOR (LOSES ELECTRON) = REDUCING AGENT
ELECTRON ACCEPTOR (GAINS ELECTRON) = OXIDIZING AGENT
redox rxns always coupled requires both

RELOCATION OF ELECTRONS
ELECTRON LOSES POTENTIAL ENERGY WHEN IT SHIFTS FROM A LESS ELECTRONEGATIVE ATOM
TOWARD A MORE ELECTRONEGATIVE ONE
RELEASES ENERGY (EXERGONIC, SPONTANEOUS)
LOSING POTENTIAL ENERGY LIKE WATER FLOWING DOWNHILL
MOVING FROM HIGH ENERGY TO LOW ENERGY
UNSTABLE TO STABLE

ORGANIC MOLECULES WITH ABUNDANT AMOUNT OF HYDROGEN ATOMS ARE EXCELLENT FUELS
NAD+ coenzyme
nicotinamide adenine dinucleotide
electron transport shuttle
oxidizing agent; gets reduced (gains electron)
TURNS INTO NADH

reduced form
NAD+ oxidized form
electron transport chain
set up gradient
oxygen terminal electron acceptor
cellular respiration
food --> NADH --> electron transport chain --> oxygen

3 metabolic stages
glycolysis
occurs in cytosol
makes small amount of atp
breaks down glucose into 2 molecules of pyruvate
citric acid cycle (kreb's cycle)
occurs in mitochondria
mitochondrial matrix
completes breakdown of glucose by oxidizing pyruvate into co2
oxidative phospohylation
most of the atp synthesis
powered by redox rxns
chemiosmosis chemical osmosis
diffusion
occurs across the inner membrane of mitochondria
inside, low ; outside, high
substrate level phosphorylation
take a substrate, remove phosphate and attach to atp

glycosis
2 major phases
energy investment phase, energy payoff phase
atp = change energy state of molecule (glucose), more reactive
step 6 first redox rxn

enolase forms PEP

FAD flavin adenine dinucleotide

electron acceptor, reduced form = FADH2 --> shuttle electrons to electron transport chain

electron transport chain

inner membrane of mitochondria
drop in free energy = energy source used to create concentration gradient
ETC does not produce ATP directly; makes gradient to make ATP

Fermentation
Glycolysis without O2

NADH NAD+
REVERSE
PYRUVATE REDUCTION
PYRUVATE GETTING ELECTRONS
OXIDATION
OXY- OXYCODONE
=HIGH
=BECOMES MORE POSITIVE
=LOSES ELECTRON
REDUCTION

REDUCE
BECOMES MORE NEGATIVE
GAINS ELECTRONS
Cellular respiration vs fermentation vs photosynthesis on test

Deamination
Process of removing ammonia from amino groups
Beta-oxidation
Breaking down fatty acid

Chapter 10: photosynthesis

Stroma dense fluid

Thylakoid
Thylakoid space
Oxygen from water; not CO2
Hydrogen oxidized
Co2 reduced

Respiration vs photosynthesis
Rs:
Electrons lose potential energy
Go down gradient and synthesize atp
Ps:
Electrons increase in potential energy
Move from water to sugar; requires energy (sunlight)
Light rxns
Occur in thylakoids
Split water, release o2, produce atp, and form NADPH
Calvin cycle
Occurs in stroma
Does not require sunlight

Dark cycle
Solar power reduces nadp+ to nadph